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- PDB-1oc3: HUMAN PEROXIREDOXIN 5 -

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Basic information

Entry
Database: PDB / ID: 1oc3
TitleHUMAN PEROXIREDOXIN 5
ComponentsPEROXIREDOXIN 5
KeywordsOXIDOREDUCTASE / ANTIOXIDANT ENZYME / PEROXIREDOXIN / THIOREDOXIN PEROXIDASE / THIOREDOXIN FOLD / PEROXISOME / MITOCHONDRION / TRANSIT PEPTIDE
Function / homology
Function and homology information


peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Detoxification of Reactive Oxygen Species ...peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Detoxification of Reactive Oxygen Species / antioxidant activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / peroxisomal matrix / positive regulation of collagen biosynthetic process / cell redox homeostasis / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / peroxidase activity / cellular response to reactive oxygen species / peroxisome / cellular response to oxidative stress / cytoplasmic vesicle / response to oxidative stress / mitochondrial matrix / inflammatory response / signaling receptor binding / intracellular membrane-bounded organelle / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / Peroxiredoxin-5, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEvrard, C. / Declercq, J.-P.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of a Dimeric Oxidized Form of Human Peroxiredoxin 5
Authors: Evrard, C. / Capron, A. / Marchand, C. / Clippe, A. / Wattiez, R. / Soumillion, P. / Knoops, B. / Declercq, J.-P.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of Human Peroxiredoxin 5, a Novel Type of Mammalian Peroxiredoxin at 1.5 A Resolution
Authors: Declercq, J.P. / Evrard, C. / Clippe, A. / Stricht, D.V. / Bernard, A. / Knoops, B.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: A Twinned Monoclinic Crystal Form of Human Peroxiredoxin 5 with Eight Molecules in the Asymmetric Unit
Authors: Declercq, J.P. / Evrard, C.
#3: Journal: J.Biol.Chem. / Year: 1999
Title: Cloning and Characterization of Aoeb166, a Novel Mammalian Antioxidant Enzyme of the Peroxiredoxin Family
Authors: Knoops, B. / Clippe, A. / Bogard, C. / Arsalane, K. / Wattiez, R. / Hermans, C. / Duconseille, E. / Falmagne, P. / Bernard, A.
History
DepositionFeb 5, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Oct 24, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEROXIREDOXIN 5
B: PEROXIREDOXIN 5
C: PEROXIREDOXIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8265
Polymers54,5823
Non-polymers2442
Water1,11762
1
A: PEROXIREDOXIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3162
Polymers18,1941
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PEROXIREDOXIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3162
Polymers18,1941
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PEROXIREDOXIN 5


Theoretical massNumber of molelcules
Total (without water)18,1941
Polymers18,1941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.195, 102.053, 145.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2175, -0.9758, -0.0243), (0.9756, -0.2181, 0.0243), (-0.029, -0.0184, 0.9994)27.5035, 19.0982, 42.4959
2given(0.2436, -0.9699, 0.0053), (0.9699, 0.2436, 0.0004), (-0.0016, 0.0051, 1)26.5877, -20.1892, 30.4133

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Components

#1: Protein PEROXIREDOXIN 5 / / MITOCHONDRIAL PRECURSOR / PRX-V / PEROXISOMAL ANTIOXIDANT ENZYME / PLP / THIOREDOXIN PEROXIDASE ...MITOCHONDRIAL PRECURSOR / PRX-V / PEROXISOMAL ANTIOXIDANT ENZYME / PLP / THIOREDOXIN PEROXIDASE PMP20 / ANTIOXIDANT ENZYME B166 / AOEB166 / TPX TYPE VI / LIVER TISSUE 2D-PAGE SPOT 71B / ALU CO-REPRESSOR 1 / SBBI10


Mass: 18193.850 Da / Num. of mol.: 3 / Fragment: PEROXIREDOXIN 5, RESIDUES 54-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LUNG / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: P30044
#2: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREDUCES HYDROGEN PEROXIDE AND HYDROPEROXIDES WITH REDUCING EQUIVALENTS USING THE THIOREDOXIN SYSTEM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57 %
Crystal growpH: 5.3
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 3350, 0.1 M SODIUM CITRATE BUFFER, PH 5.3, 1 MM DTT, 0.02 % (W/V) SODIUM AZIDE
Crystal grow
*PLUS
Temperature: 291 K / pH: 5.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %(w/v)PEG33501reservoir
20.1 Msodium cirtate1reservoirpH5.3
31 mM1,4-dithio-DL-threitol1reservoir
40.02 %(w/v)sodium azide1reservoir
510 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8441
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 2002 / Details: PREMIRROR, BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8441 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 38821 / % possible obs: 96.9 % / Redundancy: 4.2 % / Rsym value: 0.047 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.2 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.332 / % possible all: 96.1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Num. measured all: 164737 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 95.2 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HD2

1hd2


Resolution: 2→72.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.139 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1933 5 %RANDOM
Rwork0.221 ---
obs0.223 36850 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.93 Å2
Baniso -1Baniso -2Baniso -3
1-4.8 Å20 Å20 Å2
2---1.21 Å20 Å2
3----3.59 Å2
Refinement stepCycle: LAST / Resolution: 2→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 18 62 3656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223657
X-RAY DIFFRACTIONr_bond_other_d0.0010.023443
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.9854944
X-RAY DIFFRACTIONr_angle_other_deg0.90138034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9633481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.81615655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024094
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02676
X-RAY DIFFRACTIONr_nbd_refined0.2350.3766
X-RAY DIFFRACTIONr_nbd_other0.2160.33341
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.5218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0960.53
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3970.323
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.380
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9131.52396
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55423825
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.73931261
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5044.51119
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.355 127
Rwork0.286 2654
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.14110.1133-0.97421.4356-0.4161.82170.14890.2075-0.0332-0.0785-0.0863-0.1409-0.17960.1513-0.06260.151-0.00450.02690.1153-0.01840.121312.1257.57526.519
21.193-0.28950.47792.8155-1.43812.7399-0.04580.12120.1268-0.3370.00920.01650.0806-0.06070.03660.0456-0.0557-0.03890.21160.04680.201716.75829.88668.488
32.0896-0.94570.5713.424-2.59172.8394-0.13560.05040.30520.28-0.0715-0.2475-0.53550.17060.20710.0931-0.03-0.020.23470.00750.195122.424-6.29857.043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 161
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B1 - 161
4X-RAY DIFFRACTION2B201
5X-RAY DIFFRACTION3C1 - 161
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.355 / Rfactor Rwork: 0.286

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